I'm more of a Brew'd guy for flavor and cost, but have to acknowledge that Coffee & Cotton has way more space.

The Lowell public library has a no food or beverages policy, not sure how much they enforce it.

UML has plenty of random study places and they sell Starbucks products. There's some nice couches at University Crossing overlooking the Howe Bridge.

Chelmsford has KJ's on Chelmsford St across from a Dunks and Java Room closer to the center. Both decent size with good coffee.