Thanks a lot for all your answers and suggestions. I am sure the speakers are wired correctly. I checked that several times.
Occasionally, when I am lazy, I play CDs using my old Sony CD CDP-CE415. It is also connected to the same amp and the speakers. The bass is much better when I play compacts. Maybe I need to get a decent preamp?
I am not expecting room-shaking bass. I just want to hear the bass when I play vinyl records.
I think I will connect the subwoofer for now until I find the best solution for my problem.
Before I make any investments I will try few things.
1. I will try to temporary swap the YAMAHA amp with my 28 years old Sony STR-D665 which has bass boost option. It sits in my basement and plays very well with my 20 something years old Sony SS-MF315 speakers.
2. I will try to use the Sony STR-D665 as a second amp for bi-amp option.
3. I will try to temporary swap Polk Audio speakers with my old Sony speakers to see if the problem with the speakers.