Is it OK to invite some work friends to my wedding but not everyone?

Yes, as long as you're thoughtful and diplomatic.  Co-workers you don't socialize with should not expect an invitation, but defuse expectations by letting everyone know early on that the guest list will be limited.  Keep the pre-wedding office chatter to a minimum to avoid any hurt feelings.  If you're close to your boss, you should invite her.  It's a courtesy that shows you value the relationship, and she'll appreciate the gesture.