My employer is a non-profit. She has owed me several months back
wages. She just filed bankruptcy 90 days ago and did not list me as
one of her debts. She told me she had no intention of paying me and
there is nothing I can do about it. She is also under estate
litigation for a new home she and her fiance purchased just before his
death. My question is which way am I best protected. To file for
4,999. in small claims and get a judgement and then file a lien aginst
her home etc. Or should I notify her trustee in bankruptcy? Other
suggestions?Time is of the essence please advise.  Thanking you in
advance, j

I don't think you file in Small Claims.  Contact the Bankruptcy court.

If you live in Ontario, canada, go to the ministry of labour.
Employees have first rights over top of secured creditors.  This may
also apply in other areas.