The default cygwin heap size is around 300MB so increasing that value will help. Some things I discovered with this:

(1) If you set the value too high, things can lock up for cygwin or the system. Be sure to stay below the system swap space less the memory of any running processes.

(2) cygwin perl seems to be built using the perl malloc which seems to request a pool of memory large enough for your request and then some. I've seen this result in an approximate 2X larger memory request from the system which can lead to OOM death much sooner than one might expect. At the very least, it can run out one large allocation earlier than one has requested...then boom.