The best accommodation websites surprisingly are not the well know international sites but the 4 local national companies of Make My Trip, Goibibo, Yatra, and Agoda
Make My Trip www.makemytrip.com
The four main Indian website gives some very good deals especially if you go onto Apple or Google maps to locate the hotel of your choice on your smartphone and one or more of the sites will show with the best deals for same or next night late booking. I managed to get a 70% reduction in the room rate by using these websites in this way. Summit Hotels had just opened a new hotel in Gangtok and I arrived soon after opening. They had high availability at the time of my last stay so they released some rooms on Yatra and I got my room for £24 which was normally £90
For the smaller hotels and B&B's, try bartering especially if you intend to take a longer duration stay as they are open to offers. Beware that these establishments may only be paid in cash. If they do use a PDQ machine, these machines are either very clunky or only sporadically work with the local telephone system.
Cast a glance to some of the recent reviews before you commit to a specific hotel or B&B and download TripAdvisor on your smartphone. TripAdvisor reviews are given more by foreign nationals then the domestic tourist. The expectations of foreign nationals are higher and these reviews could be more objective for you.
There is a new kid on the block, AirBnB has arrived in Sikkim and some of the smaller hotels are using this facility. This is another way to market their wares but gives the more personable and smaller establishments, a great platform to gain profile and to be found. I like to stay in the more homely places away from the city centre of Gangtok and this is a great option to do that with rustic home stays and houses to rent. I take a flight from London Heathrow to Delhi and then another internal flight to Bagdogra in West Bengal. Its then a 5 hour jeep journey to Gangtok and all I want to do is to rest for a day or two in a hotel like the Summit, close to MG Marg. After a few days, I prefer to stay further afield and in a home stay overlooking the natural beauty of the local landscape.