Upgrade (SWAP) to used LS (non-vtec) or fix current D16y7 non-VTEC ?
 

I have a 1998 Honda civic LX D16y7 non-VTEC with 235k miles on it and the crank shaft bearing broke. its runs but knocks.

MY mechanic suggesting to replace crankshaft with All 4 pistons and bored 20 rings, water pump, timming belt and all seals for $900. or i can do a used LS Full swap from junk yeard for $1500. both cost includes labor. What route would be better in the long run. if i do the swap then i will do teh seals and timing .. more money ..but is it worth it ?

Keeping the small engine will give better MPG. It also seems kind of pointless to swap in a non-VTEC engine if the object is to go faster.

You could also consider a simple R&R with a used D16 engine.