How can I move massive buildings in-game in Minecraft?

If you don't mind "cheating", the easiest way would most likely be using MCEdit or WorldEdit. If this building is massive like you say, it would take a very, very long time to move it above ground using pistons. If you really wanted to do this, though, you would put a piston under a block, activate it with a lever, place a block in the new empty space, and repeat. Unfortunately, since you are supposedly underwater, this would be very difficult.

However, I have done testing, and if you were to push a column of blocks up using a piston and one of them is a water source block, the water simply disappears.

Edit: Now that I see you're an admin on a Minecraft server, I'll give you WorldEdit instructions. To use WorldEdit, first install it on your server. Then use the //wand command to give yourself a Wooden Axe. Use this to left-click on the bottom-leftmost block of your building, and right-click on the top-rightmost block. This encloses your building in a "selection". From there, you can //copy and //paste it wherever you please.