We had our pictures taken at Post Office Square right in front of the Langham Hotel in boston. It is a nice small park but also within the city so you can have both park and city photos just steps away from each other. There were hardly any other people about and is pretty secluded.
Some great shots have been done in front of the old state house - click this link http://www.parmarphoto.com/index2.php - go to gallery 3 picture #3 (I LOVE this picture especially at night, it's gorgeous!)
Also, some other shots down at the seaport (near the intercontinental hotel in Boston) click this link http://www.parmarphoto.com/index2.php go to gallery 2 picture # 2
The Charles River Bridge and The Massachusetts State House steps would also be fabulous shots too! Hope that helps! Congratulations!
I would say the charlestown navy yard has great city views. There are also some nice parks for good shots there too.
What about near Rowes Wharf? There are some great cityscapes, water views, and there is also Christopher Columbus park with the beautiful awnings. It's a great spot!
I actually just eloped but had a professional photographer (who was incredible!) We got married at the old state house and then drove around to various locations (Fenway, reflecting pool at the prudential, commons, beach, beacon hill, river) and the pics are incredible http://clients.iamwhatisee.com/Weddings/Wedding-ElaineGregor/11794325_bc4ap#837745946_4aDwn
Hopefully this will give you some ideas.
A couple of things- we were told after taking a few pictures near the reflecting pool that you aren't supposed to take wedding pictures there, but if you can do it quickly enough, it's obviously worth it.
The commons is obviously crazy busy, but the bridge there is worth it.
We were overlooking the boston sky line right across from MIT.
Highly recommend going to Fenway if you're a sox fan, we really wanted to get a picture with the banners on yawkey, but they weren't up yet (March).
If you are looking for a photographer still, Patrick is incredible!
castle island in south boston. They have the old band stand and the sugar bowl gazebo and of course the castle itself!
Click on each tool to see a sample.