I have a yakima rack and basket. Works well and once set up is easy on or off.
Roof baskets?
I have just the SR5 model, I do not think I have anything on top to mount anything, how will I go about mounting a basket up top?
On the 2005+ you can pull the rubber molding up and there are holes for mounting part of the factory rack. IIRC, one of the rear holes isn't drilled or something like that.
On the access cab, there are no holes from the factory, that is only on the double cab. For the access cab, you will need to drill holes and install some blind nuts.