As a former Boston area college student myself (who actually took my now-wife on our first date to Top of the Hub), I will say that your impression of the Top of the Hub is pretty much on point; it has a great view if it is not cloudy and the food is fine though a bit overpriced.
Craigie on Main is a pretty solid call; though I have never been, it is a go-to for friends who still live in town. A couple of other options which might not be as fancy but are places I have enjoyed: Oleana, a great Mediterranean place in Cambridge, and Legal Harborside in the seaport area.
Oleana is not going to be as expensive or fancy as you might be looking for but it has great food and a mezze menu that allows for a lot of interesting food to be shared. It also has lots of vegetarian options, if that is needed.
Legal Harborside is part of the Legal chain, but the second floor of this restaurant has great water views and a more sophisticated menu with an obvious emphasis on seafood (we had our rehearsal dinner here).
Have a great time, graduation weekends in Boston are a hectic whirlwind but hopefully you will have time to enjoy it!
Oleana
134 Hampshire Street
Cambridge, MA
oleanarestaurant.com
Legal Harborside
270 Northern Ave
Boston, MA
legalseafoods.com/restaurants/boston-legal-harborside