Neither. Polk's subs are average at best. Take a look at the offerings from HSU, Adire and possibly even SVS, depending on your budget, for your money. What is your budget anyway?
I bought the same system last spring from CC for $609 with the PSW303 included. I auditioned several other ultra-compact 5.1 set-ups (all street priced under $900) and to my ears, it was the best of the bunch. I could have upgraded to the PSW404 for an additional $100, but didn't feel my needs warranted spending the extra dollars as the room I have the speakers in is very small. Given that the PSW404's amp, rated at 200 watts, has twice the power and a 10" driver versus the 8" driver in the PSW303, it would probably make sense to go that route if your room is of medium to large size. Since the sub is powered, your choice of either Yamaha receiver should be fine.
I agree on the consensus on the Polk subs. I also started with a Polk RM series "Home Theatre In A Box" set-up. Sounded ok, but from the first time I fired it up, I didn't like the woofer, and noticed it was underpowered and tended to bottom out easily. It now augments my alternate set-up in my "play" room. With a set of crappy no-name towers and a KLH reciever with a Sirius set-up.
I ended up with a inexpensive Sony WA500 sub. Much better, and not much money more.
if you go for polk sub, get the 404 to up the frequency (make up for limited freq resp on those sats.) for best results SVS sub if you can afford it (start at 599, same price as those polks) or check out rava subs, lots of SVS fans like em. btw onkyo recievers love polk.