First tip - they are the Isles of Scilly, NOT the Scilly Isles.
Tresco, Bryher, St. Martins - good visits. The island postman is worth photographing - I did a full feature on them about 10 years ago (remember me to them!) They use a RIB to deliver the post about the islands!
The best boat trip is with Mark and Susie Groves are the outfit to go with, Island Sea Safaris. Another one I did a feature on, many years ago now. They will get you within a few feet of seals and they will take the RIB in close to the rocks. There is an underwater camera amidships too, with large screen so you can see the seals and birds underwater.
One and All.