Some reference points:
★★★: most expensive
★★: relatively less expensive
★: least expensive
Hotel Kanra Kyoto★★★
http://www.hotelkanra.jp/en/index.html
http://www.hotelkanra.jp/
Hotel Anteroom Kyoto★★★
http://hotel-anteroom.com/
Monbou Kaikan★★★
http://monbou.jp/index_e.shtml
http://monbou.jp/
Hotel Granvia Kyoto★★★
http://www.granviakyoto.com/
http://www.granvia-kyoto.co.jp/index.html
Rihga Royal Hotel Kyoto★★★
http://www.rihga-kyoto.co.jp/index.htm
Dormy Inn Premium Kyoto Ekimae★★★
http://www.japanican.com/hotels/shisetsudetail.aspx?st=6231A11&ref=dormy
http://www.hotespa.net/hotels/kyoto/?gclid=CL3WosXhm6oCFahLpgodqypExA
New Miyako Hotel★★
http://www.miyakohotels.ne.jp/newmiyako/english/index.html
http://www.miyakohotels.ne.jp/newmiyako/index.html/
Daiwa Roynet Hotel Kyoto-hachijoguchi★★
http://www.daiwaroynet.jp/kyoto-hachi/
Kyoto Century Hotel★★
http://www.kyoto-centuryhotel.co.jp/english/index.html
http://www.kyoto-centuryhotel.co.jp/cgi-bin/cms/index.cgi
Kyoto Tokyu Hotel★★
http://www.kyoto-h.tokyuhotels.co.jp/en/
http://www.kyoto-h.tokyuhotels.co.jp/
Hotel Hokke Club Kyoto★★
http://www.hokke.co.jp/2601/
Kyoto Tower Hotel★★
http://www.kyoto-tower.co.jp/tower_hotel/english.html
http://www.kyoto-tower.co.jp/tower_hotel/
Apa Hotel Kyoto-ekimae★★
http://www.apahotel.com/hotel/kansai/01_kyoto-ekimae/english/index.html
http://www.apahotel.com/hotel/kansai/01_kyoto-ekimae/index.html
Hotel New Hankyu Kyoto★★
http://www.hankyu-hotel.com/cgi-bin2/cms2/index_en.cgi?hid=30kyotoshh
http://www.hankyu-hotel.com/hotel/kyotoshh/index.html
Apa Villa Hotel Kyoto-ekimae★★
http://www.apahotel.com/hotel/kansai/02v_kyoto-ekimae/english/index.html
http://www.apahotel.com/hotel/kansai/02v_kyoto-ekimae/index.html
Kyoto Daini Tower Hotel★★
http://www.kyoto-tower.co.jp/daini_tower_hotel/english.html
http://www.kyoto-tower.co.jp/daini_tower_hotel/
Urban Hotel Kyoto★★
http://uh-urban.com/kyoto/contents/english/index.html
http://uh-urban.com/kyoto/index.html
Kyoto Daiichi Hotel★★
http://www.kyoto-1-hotel.jp/english/index.html
http://www.kyoto-1-hotel.jp/index.html
Kyoto Plaza Hotel★★
http://www.kyoto-plazahotel.co.jp/
Super Hotel Kyoto Karasuma-gojo★
http://www.superhotel.co.jp/s_hotels/karasuma/karasuma.html
K's House Kyoto★
http://kshouse.jp/kyoto-j/
Some reference points:
★★★: most expensive
★★: relatively less expensive
★: least expensive
Kyoto Hotel Okura★★★
http://okura.kyotohotel.co.jp/english/
http://okura.kyotohotel.co.jp/
Kyoto Brighton Hotel★★★
http://www.brightonhotels.co.jp/kyoto/en/index.html/
http://www.brightonhotels.co.jp/kyoto/
Hotel Nikko Princess Kyoto★★★
http://www.princess-kyoto.co.jp/english/index.html
http://www.princess-kyoto.co.jp/index.html
Mitsui Garden Hotel Kyoto Shijo★★★
http://www.gardenhotels.co.jp/eng/kyoto/
http://www.gardenhotels.co.jp/kyoto/
Hotel Monterey Kyoto★★★
http://www.hotelmonterey.co.jp/en/htl/kyoto/index.html
http://www.hotelmonterey.co.jp/cgi-bin/portal/cms/hotelindex.cgi?hid=monkyo
Village Kyoto★★★
http://hotel-village.jp/kyoto/eng/
http://hotel-village.jp/kyoto/
ANA hotel Kyoto★★★
http://www.ichotelsgroup.com/h/d/6c/1/en/hd/kstna
http://www.ana-hkyoto.com/
KKR Kyoto Kuniso★★★
http://www.kuniso.com/
Rhino Hotel Kyoto★★★
http://www.rhino.co.jp/english/index.html
http://www.rhino.co.jp/
Karasuma Kyoto hotel★★★
http://karasuma.kyotohotel.co.jp/english/
http://karasuma.kyotohotel.co.jp/
Hotel Harvest Kyoto★★★
http://www.resorthotels109.com/en/kyoto/
http://www.resorthotels109.com/kyoto/
Royal Park Hotel The Kyoto★★★
http://www.rph-the.co.jp/kyoto/
Kyoto Garden Palace★★★
http://www.hotelgp-kyoto.com/english1
http://www.hotelgp-kyoto.com/
Hotel Toyoko Inn Kyoto Shijo Karasuma★★
http://www.toyoko-inn.com/eng/index.html
http://www.toyoko-inn.com/
The palace side hotel★★
http://www.palacesidehotel.co.jp/english_site/
http://palacesidehotel.co.jp/
Hotel Mystays Kyoto Shijo★★
http://www.mystays.jp/location/ms_kyotoshijo/
Best Western Hotel Kyoto★★
http://www.bwjapan.co.jp/kyoto/en/index.html
http://www.bwjapan.co.jp/kyoto/index.html
Kyoto Kokusai Hotel★★
http://www.kyoto-kokusai.com/e/index.html
http://www.kyoto-kokusai.com/index.html
Kyoto Kokusai Hotel★★
http://www.kyoto-kokusai.com/e/index.html
http://www.kyoto-kokusai.com/index.html
Mitsui Garden Hotel Kyoto Sanjo★★
http://www.gardenhotels.co.jp/eng/sanjo/
http://www.gardenhotels.co.jp/sanjo/
Hotel Unizo Kyoto★★
http://www.hotelunizo.com/eng/kyoto/index.html
http://www.hotelunizo.com/kyoto/index.php
Hotel Oaks Kyoto Shijo★★
http://www.h-oaks.co.jp/kyoto-shijo/english/index.html
http://www.h-oaks.co.jp/kyoto-shijo/index.html
Ark Hotel Kyoto★★
http://kyoto.ark-hotel.co.jp/index.html
Viainn Kyoto Shijo-muromachi★★
http://kyoto.viainn.com/
Kyoto Central Inn★★
http://www.kyoto-centralinn.jp/
Kyoto Horikawa Inn★★
http://www.horikawa-inn.com/
Kyoto City Hotel★★
http://www.kyotocity-hotel.com/index_E.html
http://www.kyotocity-hotel.com/index.html
Hotel Sunroute Kyoto★
http://www.hotel-sunroute-kyoto.co.jp/
Super Hotel Kyoto Shijo-kawaramachi★
http://www.superhotel.co.jp/s_hotels/shijyo/
Hotel Gimmond Kyoto★
http://www.gimmond.co.jp/kyoto/english/e_index.html
http://www.gimmond.co.jp/kyoto/index.html
Court Hotel Kyoto Shijo★
http://www.courthotels.co.jp/kyoto/
City Pension Le Liond'or★
http://www.leliondor.jp/
Hotel Alpha Kyoto★
http://www.japanican.com/hotels/shisetsudetail.aspx?st=6230028&ty=rsv
http://www.alphakyoto.com/
Kyoto Rich Hotel★
http://www.rich-hotels.co.jp/kyoto/
For more possibilities, the following search links would be useful if you're familiar with Japanese websites:
Jalan
Rakuten Travel
Ikyu.com