My personal favourite is Hotel Ganesha Inn. The room tariff is pretty reasonable; the rooms are excellent, offering a splendid view of the river.
They arrange rafting trips for their guests; no need to look around for a reliable rafting troop.
The hotel staff is polite, always ready to help you with everything. As we had a late night bus to catch while coming back from Rishikesh, the manager personally took charge and arranged for an auto, so that we can reach the terminus, without worrying about our safety.
A word of caution: there are many home-stays in Rishikesh, promising "mountain view" and calmness, being away from the bustling city. Do not sign up for them!
We initially put up in one such place, which we had booked from Delhi. The place is literally far from the main centre, meaning that for only to feed yourself, you have to travel at least twice for 30 minutes to reach the main point which is Laxman Jhula. Now if you are spending only 2 days in a town, you surely wouldn't want to spend minimum 2 hours everyday going up and down a dusty road only to have your lunch and dinner!
Plus, the place we chose was right beside a garbage heap. Perhaps, by "mountain view", they meant view of the mountain of accumulated trash.
Just don't fall for the cozy pictures you get to see in their websites.
Where to eat in Rishikesh