I'm thinking about telling my roommate that her boyfriend can't be here all the time.
Why don't you want your roommate's boyfriend here all the time?
He's here too much and it makes me uncomfortable.
It's fine for you to tell your roommate that her boyfriend is at your place too much. It's not right for someone to assume that their partner can stay at their place all the time to the objection of their roommate.
I'm just going to suggest it.
That sounds like a polite way to handle it. Be sure to stand your ground, because it's your living space and you deserve to feel comfortable there.