The Yakima rack is plenty good enough for both your surf boards and snow boards, its also fine for canoes kayaks and bikes. Yakima and Thule both make equivalent products for similar amounts of money. Most of the parts you buy for setting up your rack system can be transfered to another vehicle at a later time (unlike most factory bought racks systems)and are compatible with many accessories. Both companies have a long history of keeping their basic design the same so almost every thing is backwards compatible and probably will remain so.
If you have a Thule rack now with rain gutter towers you should be able to save the cross bars and buy a set of tracks and towers from Thule that do the same thing as the Yakima system. This might save you some money and help keep all your rack parts and accessories compatible. Though these days both companies actually make the attachment points for most things to work with either the square or the round bars. As others have noted there is drilling involved and its worth making sure you use good silicone on it. Triple check your measurements of course, nothing would blow worse on this project than to muck up hard top.
The down side to either of those two racks is that their weight capacity will never be greater than 165 pounds including the weight of the racks(by the book) this is the ultimate rated limit according to the manufacturers regardless of vehicle. I don't know how much its rated to on the hard top. Most people my self included ignore the weight of the racks in that calculation and often go a little into the safety buffer. Gross overloading (usually more than double the limit) while driving with sudden acceleration, deceleration, and hard turning can and has led to racks and or their contents being ripped off. This isn't very common but keep in mind that the heavier and taller something is that you put up there the more sail area and leverage it will have on the rack and your roof. Your boards are small and light so no problem there, but if you strap two tandem kayaks to the top don't drive it like a sports car(we used to carry two expedition boats on our XJ with no problems). Very few people manage to do this but about once a year we would get some one who thought the laws of physics didn't apply to them and that their racks should be replaced for free(used to work at REI, sold many many racks).
Meyers pointed out the racks that are frame and body mounted. These can have weight capacities of up to 800 pounds. If you want to strap a dead moose to your jeep thats the way to go, they also do camping gear or work well for cross country moves. I think most of them will cost more and be taller(not sure if garage clearance is an issue yet). If you're just hauling the items you mentioned before these racks will be over kill. Also they can complicate top removal though some of them fold down or have quick disconnects to help with this. You can also mount the tracks on your roof and do a frame rack over them later on if you need.
Personally I'm not drilling holes in a hard top and certainly not for a relatively low weight capacity, so I'm looking ahead to one of those frame racks with a little ladder so I can climb on top and set up a tripod or something. In the mean time I'll be getting a Yakima swing away hitch rack for my bikes and use their attachment to convert it to skis and snow boards this winter. You might check out that option too.