Can't help with hotels as I've never stayed in any in Inverness, too near home.
It depends a bit on the time of year you'll be here and whether you are going to be hiring a car or relying on public transport. I'd advise hiring a car, which you should be able to do from Inverness Airport, public transport is not that brilliant for moving between some of the best wildlife areas.
Loch Ruthven RSPB reserve south of Inverness is great for Slavonian Grebe, Red Throated Divers and fishing Ospreys in the spring and summer.
Loch Garten RSPB reserve for Crested Tit and Red Squirrels, as well as Osprey, Goldeneye and Capercaillie. There are also some ponds in the wider forest area which are great for dragonflies and damselflies, including the more unusual White-Faced Darter and Northern Damselfly.
The Rothiemurchus estate near Aviemore is good for a variety of birds, mammals, flowers and insects. There is an outside chance of seeing a Wildcat as well.
You might want to have a look at the following link to a thread which has some good suggestions for the Cairngorms and surrounding areas.
Wildlife watching in Cairngorm