I would just go with the Yakima aftermarket roof rack, but then I would need another rack accessory for snowboards, and then another rack for bikes. No way am I wrestling my mtb on to the roof of my FJ.
That said, the stock rack is ok but you still have to add another rack on top of it to actually hold anything. Get's really tall in a hurry and still doesn't accomodate bikes. That, and I don't like the looks of the stock baja rack.
So, I got the off-road package with suspension and locking rear diff but I skipped the rack and rock bars.
In any event, Yakima and Thule both make nice bike racks with an additional attachment for snowboards. They are just a little expensive. Although cheaper than a roof rack and attachement just for boards. Probably going to go with something like this:
Congrats on the FJ purchase, we love ours and it was just rated #1 by Kelly Blue Book for resale value!
Funny we love our rack works great for hauling canoes\kayaks and our giant Thule box fits great up there.
Wouldn't mind having a hitch mounted basket type thing for hauling random extra shit though and for our yearly migration to Utah and back, I'v seen them for a couple hundred bucks.
What about something like this?
Curt mfg., Hitch mounted, folding cargo carrier - By Curt Mfg
500lb weight capacity should be plenty