Glad to hear your wife is accepting of the poly situation. I'd have a sit-down with her and say something along the lines of:
"My main concern is family time. I want to make sure that our daughter is getting enough time with both parents. Over the last few weeks you've spent a lot of time with your boyfriend, and I feel like our daughter isn't getting enough.
I don't personally want to put restrictions on your relationship, but I do want to make sure that we as a family are getting enough time. I don't want our daughter to end up with a single parent scenario every other day. I'm not quite sure what the solution is for this."
Get some feedback from your wife about how you feel, keeping in mind that she is probably experiencing some NRE (New Relationship Energy). Whatever solution you come up with must be fair to everyone.
Good luck; hope we can help.