Can I extend my 90-day entry stamp in Thailand without leaving the country on a multiple entry Non-B visa?

YES, you can apply for the 1 year Extension of Stay based on employment in Thailand.

BUT you need to meet some simple requirements, like salary payments to staff, paying income tax and a few more, visit your Immigration Office to get the list of requirements, tell your staff to start up the copy machine, tick the list when copy is made and when all done, go back to apply.

AFAIK, from Non-B multiple visa entry, the only available extension is a 1-year extension based on employment, by both your company and you meeting the requirements for a 1-year extension. What I understand is (or was) you don't have to wait until the last entry from the visa, you could apply for an extension on any entry from that visa. But as said above, go to talk with your local immigration office about the possibility. Otherwise, you need to bounce.

As you have a multiple entry visa, you can enter Thailand on the very last day of the visa sticker to be stamped for another 90 days, btw.

You could ask your local immigration if you could do your yearly extension based on employment early.