Can PERM based green card be filed after 3 yrs on H1b in my J1 waiver job rather filing now ?

Although I recommend that you start the PERM process as soon as possible you can wait to apply for your PERM application. I would recommend that you start the PERM green card process early because the entire green card process usually takes more than one year. You can extend your H1B beyond the six year limit if your PERM application has been pending for more than one year. Additionally, if your I-140 is approved but you are unable to apply for your I-485 green card you could extend your H1B in three year increments. If you wait until your 5th year in H1B status you may not have enough time to take advantage of these benefits while maintaining legal status in the U.S.