Thru bolt and use the biggest washers you can find to back it, the bigger the better. As stated above, overbuilding it is best, and make sure to use a good sealant to coat the bolt hole and keep the hardtop water tight. Also as a side note, my antennas were mounted with a soft sponge like gasket between the metal mount and the hardtop, well after a few seasons something has happened and now they leave black streak's everywhere on my hardtop and down my cabin. My antenna mounts were not caulked around the base, I would recommend a clear silicone or GE Silicone II in Almond(red label) to seal it and keep this from happening, as well as keep water from seeping under the mount over time. As stated above, overdoing it is the best way and in the end typically saves you work.
Also as mentioned above, make sure you can reach the antennas without climbing on the top, mine are mounted only a few inches from the edge of the hardtop, just on the outside of the hardtop metal work, makes them easy to reach and lay down or put up, my center antenna(I have 3) is a pita to reach, I have to hang on my hardtop to reach it. Wish the previous owner was a little more conscience of this and moved it forward a few inches infront of the hump to make it easier to reach.
Good luck with the new boat!!