You can take your pick of core materials, depending on what you want to pay. But marine ply is fine. There are various grades, you don't need the best, but might as well get it, since price difference is worth it. Should last the life of the boat if you do it right.

If your deck is still good, it will go bad eventually if you're not careful. The best thing you can do to preserve your deck and fuel tank is replace all those seive-like snap-in deck plates with proper Becksons with screw-on lids. Bed them well in 3M 4200 or Sika equivalent and keep the 0-rings fresh.
When you remove the old deck plates follow West System procedure for mounting deck hardware, i.e. remove exposed core around the edge of the hole and pump thickened epoxy into the groove. *If you do that, even if your deck plates leak, no water will get to the core. More $1,000 projects begin because of through deck fittings (stantion screws, cleat hardware, etc.) that leaked into the core. No exposed core -- no problem.

Likewise, if your replacing the core in your deck section, use only solid glass at any spots where through-deck hardware will be mounted. Most good yachtbuilders follow this procedure so as to avoid the soaking core problem altogether.

Here are some core manufacturers:
http://boatdesign.net/Directory/Mate...mposite_Cores/