Anything in the airflow path will help... but the gains will be small. You can upgrade your intercooler, ported intake manifold, upgraded intake elbow, upgraded exhaust manifolds, cam, etc... I am assuming you are running a t4 kit? Right?
If it is a box s366 then you could upgrade to one of the fmw or sxe turbos.
Before switching injectors, turbo, or cam... I would definitely try a couple different tunes. I have been working with a lot of Non-vgt guys and TSD tuning and they have all been very impressed. Most stated they were the BEST TUNES they had ever run... but every truck is different and people prefer different tunes.