1999 5.2L 5 speed standard.

Take it to tranny shop clutch was replaced, tranny was re bearing /syncro'd. I told them I thought transfer case was making noise, So when they had tranny out then took the transfercase apart to make sure everything was good. Resealed it, I can see the new sylicone or whatever they used. Transfer still makes a bit of noise sitting there at idle in neutral, is this normal or should it be silent?

 

a little noise is normal. Thing to do is get an automotive audioscope and pinpoint which area of the transfer case is making the noise, which will help you determine which component is out of spec.