If it's just running (not a daemon) then just use Ctrl-C.
If it's daemonized then you could try:
$ ps aux | grep node
you PID 1.5 0.2 44172 8260 pts/2 S 15:25 0:00 node app.js
$ kill -2 PID
Where PID is replaced by the number in the output of ps.
Hope it helps!!