My sister is bipolar/Borderline, she is not taking medication and has started a relationship with a man in NY she just met last month. (divoricd 3 times, many kids)
She is planning on moving next month from PA to NY (on canada border) and marry this guy (who lost custody of his own children and a has a DUI arrest).

She has my 7 year old nephew. He has moved from Florida, to NJ, to Florida, to PA and soon NY in less than 5 years.

He currently is under the primary care of his grandmother, although she does not have custody. (his father says he does not want him)

I recently witnessed my sister lock herself and her son in a room, while she was having a fit, and she needed to be talked down. She will not listen to reason and is irational most of the time.

Do I have any rights to either, keep my sister where we can "monitor" her with her son, or can I take custody?

It would appear from your post that your grandmother is responsible for your nephews well being, is she aware of the situation, if not I think you need to bring it to her attention.
Would she be allowed to take your nephew being that your grandmother has primary care,or is it just a case of giving permission?

Your sister has only known this man a matter of weeks,and I have to say judging by your info he doesn't sound a very admirable person,his history leaves a lot to be desired,quite honestly I wouldn't want my sister yet alone my nephew going off with him.

I think you should seek some legal advice on this matter, just to see what your rights are concerning your nephew.The care and welfare of this lad has to take priority, especially with your sisters condition.

I think you need to look out for them both,although I doubt she'll see it that way.
If his Mum (your sister ) is perfectly capable of caring for her son (nephew) it maybe you haven't a leg to stand on.
However if there is an issue over care and welfare of your nephew, then you could have a case.

Seek legal advice on this matter.