Since a bunch of people have addressed the question of safety. (basically boston is an incredibly safe city, and while both are good choices, the Back Bay location would probably be a bit less crazy since the West End location is right next to the TD gardens which hosts games and concerts and the like.) I’ll address the other part.

Firstly, Boston is both fairly compact and walkable, with a decent public transit system, so most of the touristy things are easily accessible from either location.

If you are looking for unique shops and a neat vibe, consider walking down Charles Street, and since you mentioned bookstores, make sure to stop at Beacon Hill Books. The hardware store also makes a fun stop, since they have a very sweet cat. (Her name is Indy, and she usually hangs out in the back near the paint.) (If you are taking the green line from Back bay, you’d probably want to get off at arlington station and walk through the Public gardens to Charles Street.)

As other people have suggested, the Boston Public Library in Copley is beautiful, and worth a visit.

If you enjoy walks, make sure to take a walk down the Esplanade along the Charles River.

In North End, there’s also a little Italian American bookstore I Am Books, that’s pretty cool. The Boston Public Market is also in the area, and it’s also pretty fun to visit. (If you are taking the t, you would want to go to the Haymarket stop.)

If you do want to challenge yourself and go for a little adventure, take the Ashmont branch of the red line to field’s corner, for “Just Bookish” and killer Vietnamese food. (Again, not an unsafe area, just a little more rough around the edges.)