I know they have whale watching boat trips out of Salem; I would have gone, but it was raining and chilly the day I was there, and I figured it would only be worse out on the water! I didn't stay in Salem either, so I can't recommend anyplace to stay.
One thing I'd recommend is to go to www.witchvox.com
and look for shops in Salem. They have state-by-state listings of people, groups and stores, so I would think there would be info (and possibly links to websites) on different shops in town.
There are a lot of tourist-trap type places there, which I avoided. I mostly went in and out of the dozens of extremely cool shops. If I were to go back, I would have to save for a while beforehand since I know I could easily drop $500 in an afternoon there if I had that kind of spare money. Cool, cool, cool stuff. More Witchy stuff than I have ever seen in one place!!!