Diesel Tank Rebuild- 5052 or 6061 ?

Both would probably be fine; but I would ask your fabricator which one is more easily welded since the tank will need to be welded along the seams and fittings welded on. I think the 5052 has better weldability and that would make it a better choice but I can't tell you for sure if it is easier to weld than 6061.

I would go with stainless steel instead of aluminum for a tank. That's just me... aluminum on a boat, sitting in the bilge can have bad things happen to it fairly quickly.

6061 T6 will work, but 5052 has more options for welding it "correctly".
6061 T6 was developed for designs where it is used as a structure (think airplane or bridge) as opposed to simple tank designs. As such the ksi is higher and is limited in weld consumables.
5052 can be welded with 4046 wire which is most common. If 6061 T6 is welded with 4046 wire, the welds will crack over time from flexing. I've seen it happen on box structures simply by moving it with a forklift.

Bottom line, yes, you can use 6061 T6, but make sure your fabricator knows the correct wire to use for the application.