I've done some research on "chuffing" for different sized ports and flares.
As brent_s points out, your velocity in the 4 incher is fine till you get to the lower end of operation.
As frequency is decreased, audible turbulence occurs at lower speeds. At 39 m/sec, you are well past the point where turbulence is occuring in the core of the port.
From my work.....
For a 4inch port "core" turbulence & compression occurs @ 20 m/sec
For a 6inch port "core" turbulence & compression occurs @ 26 m/sec
Moving to a 6 incher drops you to 18 m/sec which fixes this problem.
The next area of concern is turbulence occuring as the "boundary" layer of air exits the port. This can be addressed by flares.
For 18 m/sec, you would need a 25mm radius flare on the port exit. The intake could be 5mm smaller. This could be done with a rollover bit in your router, or you could use commercial offerings, such as the PSP flares.
All of this assumes that you're wanting to feed your sub with 17hz at the same level as content higher up the spectrum. In practice, content this low is usually at a lower volume. In this case you could drop your flare radius to 19mm, which is more in line with what sonosub builders have been doing for ages now.
See the links on my
Port Flares page for more detail.
If you're building a sonosub, grab a copy of
sonosub.exe - it will tell you your port resonance at a glance.