My visa (Non-B multi) is soon to expire but my last entry stamp lasts longer than that (it is 90 days since last entry). When should I apply for a new visa to get another year? Can I rely on stamp date or better stick to visa date? My lawyer cannot answer the question unfortunately. Maybe someone here had this situation before. Thanks.

The date the 90 days ends is what is important. You could even go out and back to get a new 90 day entry  on or before the enter before date on your visa which is the date it expires.

If you are getting your visa in Penang your work permit may be more important than anything else. You have to be sure you have at least 8 months remaining on it when you apply.