Is there a metal nipple to replace plastic nipple on intake leading to heater core

Probably. Try your local auto parts store and hardware store.

I found 3/8 pipe thread with 5/8 barb for heater hose but the problem I see is the plastic manifold is stressed and nearly cracking. My concern now is that the manifold will crack completely, leaving me with no choice but to buy a new manifold. The outlet isn't much bigger than 3/4 inch altogether, the walls are very thin after tapping it out for threading the pipe fitting into it.

There is only so much you can do. Use teflon thread sealant (type in the bottle) and don't over tighten and hope for the best.

So.. Have you done it, or you just replaced the manifold?