Find Long Wharf, right next to the Aquarium. There's a cruise line that does cruises out to the islands, scenic cruises, and even sunset cruises. Highly recommended. The islands are beautiful. http://www.bostonharborcruises.com/
and http://www.bostonislands.com/default.asp
The Spirit of Boston for a dinner/sunset cruise is not shabby at all. http://www.spiritcitycruises.com/boston/bridge.html
For night time reflection shots it's tough unless you're on a boat. Check the places above for a sunset cruise.
You could go to East Boston. Here's a Mapquest
link to the area that would make for good city shots. Lewis Street and the area. However, I don't know that neighborhood at all. Use your judgement.
For boats in the harbor a very good place is Fort Independence Park. Mapquest
. You're right across from the airport where the channel is at it's narrowest. Getting off on one of the islands - like George's Island, the old Civil War Fort - is a good bet, too.
To really get some good boat shots you might want to try Gloucester Harbor. It's about 1.5 from the city, but it's got a *lot* of stuff around, and the harbor gets tight. Stage Fort Park is the Gloucester area visitor's center, with great views of the harbor. Mapquest
Gloucester is more inclined towards fishing boats, though. But I could send you on a day trip around Gloucester that would have you reeling with photo ops though. Let me know. It's not Boston proper, but it's all classic New England seacoast.
More nice shots and small sailing craft and crew boats - the Charles River. Walking the Esplanade right along the river is very nice. You face Cambridge, but can walk over one of the bridges to the Cambridge side for Boston shot. Shots from the bridges are worthwhile, too. Mapquest
- note all the green on both sides of the river - public land and walking paths and such.
The boston Public Gardens are interesting for a short visit. The Swan Boats are world famous. Same map as above, on the right side - "Public Gardens."
The Constitution - Old Ironsides - is in Boston National Historic Park. Mapquest
Around the harbor from land, if you've got the time...
Mapquest
Fort Dawes is also known as Deer Island. There's now a big ugly sewage treatment plant on the island, but the park near it allows for nice harbor view. The tip of Hull has a lighthouse I believe. More harbor shots, and Hull is a busy boating/sailing area. You gotta have time for those 2 places - they're both an hour from the city proper.
If you only do one thing, take a half day and do a cruise or two around the islands.
If you're looking for anything more particular, just ask. I could name hundreds of "places of interest" but can get more specific if you let me know what kind of stuff you're interested in.