If you say your tranny already doesn't feel that good then I would recomend that you don't do anything to your truck until you get some aftermarket parts in it or get it replaced. It's going to be expensive, there's no way around that. If you add power to a good tranny, you're pushing it too hard, if you're adding power to a not so good tranny, you're asking for trouble with it. Having said that, between the two choices you're asking about, I would go with the programmer. It adds fuel and timing to get its power where the injectors just add fuel. The timing is better for the engine. Also, you should look at an aftermarket lift pump. The stock one won't support either of those mods and will end up killing your VP44. VERY EXPENSIVE!!!
Just to give you an idea of what kinds of repairs you're looking at if you don't start with the tranny and lift pump.
New VP44- $1200 just for the pump. Then you have to pay labor to get it installed.
New tranny- $3000-7000 depending on what tranny you decide to go with.
This is just my opinion but i'm sure that most people on here would agree it.