Will a MS with ~3.7GPA with good research experience and strong recommendations offset my horrible U-GPA to get into PhD?
It is good to aim high. It is also good to have broad target. If you apply to only a few schools with very similar profiles then being rejected by one will probably have a similar outcome at the others. So, I recommend a range of schools if you really want a degree and not just bragging rights about a top 50 school. 

But, about your GPA. It isn't a plus, of course, but most (not all) people who evaluate your application will weight the more recent work as more important than the earlier work. Therefore, if your recent work is good and you have letters that attest to the quality of your work and your dedication, then the older numbers will be discounted by most. 

But, the competition is still very strong and the slots are few. If someone has to make a choice between two candidates, the choice has to be made and lower priority things may bear some weight. 

However, the only way to know whether you have a problem is to actually make application to some places and then evaluate the feedback. There are some questions, like this one, that can only be answered by actually trying. But, you will be more likely to get accepted somewhere if you don't target too narrowly.