The cradle in PE could be a good solution as suggested by Pauillac, however if this does not work and I doubt that a two years old will lay quiet so long, then I would probably go for the 4 seats in Y. Removable armrests are quite nice if you have the whole row for yourself. Don't expect a better service in PE, it's Y food with Y service, you get however an amenity bag and leg space is indeed better than in Y.
You could also gamble and take 3 PE seats and hope for a cheap ugrade option to Biz when checking in, but you should not depend on this. I have no idea if SFO-CDG is easy for such (paid) upgrades.