I will assume that most of your traffic is wireless (if it is wired definitely wire back to common switches).
I've gone both ways for wireless and gotten good results -- it really depends on the area layout and where the users are cluster/spread and how many APs you're talking.
Just two or three consumer quality APs should make no difference, but as you get into larger numbers or commercial units it is an advantage to run them all back to a switch/switches, this is of course even more true if you use PoE ceiling mount APs and you use a PoE switch instead of individual injectors that really simplifies things.
Connection to the router isn't really the way to go since all your intranet traffic works through common switches if you go...