I live in PA & work in PA, but the company is based in NJ. I currently pay PA withholding, NJ SUI, NJ SDI and NJ FLI. Is this correct?

Yes, you have PA income and must report it on PA state tax return. Your income is not NJ income and you do not pay any NJ tax.
If you are present in NJ to work, you have NJ income. Your U.S. Tax Return: Working or Living in Two or More states (http://taxipay.blogspot.com/2008/06/working-in-two-or-more-states.html)

You should NOT be paying NJ SUI, SDI and FLI, since you do not work in NJ. It doesn't matter where the company is based. Talk to your employer to get them to stop that.

I work from home in Tx but I work for a NY base company where do I pay taxes?

You pay taxes to the state in which you live, and also to the state in which you work (if different). So if you don't live in NY nor are physically present in NY for work you do not pay anything to NY. And of course since TX has no income tax you don't pay anything there either.

I know you didn't ask about this, but if by chance your employer has been withholding NY income taxes it's a mistake, and you should get them to stop immediately. To get your money back you would have to file a non-resdient NY state income tax, which would show $0 NY-source income abdnd hence you get a full refund.