Got a 2011 FXDC with 30K's on the clock. Recently it has starting to make a squeaking/whining noise when riding. No noise at low speed, intermittent when going a bit faster and constant when doing 50K/h plus. Hard to tell where it's from - sounds in the front. Is independent from the engine and no, not brake pads as the sounds doesn't change when pulling the brake lever. Haven't found anything rubbing against wheel or belt so a bit at a loss.

Sounds like a wheel bearing to me. I had mine pack up at 19 years old and it took a shop 3.5 hours to get the old ones out and replace. The job did include disc replacement and I removed the wheel at home. Yeah, I know my bike is an antique but its mine. Mine were growling rather than squeaking. Shop had quoted the job at $54 labour plus parts and they stuck to the quote. Very impressed!

Jack the front wheel off the ground and spin the front wheel.....

^^ What Pauly said^^   also grab the top and bottom/or back and front of the wheel while it is off the ground and see if there is any play side to side with the forks held firmly.
Would have thought a rear wheel bearing would shit itself first if they had never been changed before.
Pressure water cleaners are the enemy of wheel bearings too. You often use one?.

Just swap them out and then you can rule out the bearing as the source of your noise. They're only $15 each trade....or...to positively ID the bearing, spray the seal and bearing with chain lube and test ride, it'll quieten down for a  while.

Probably $54 per hour. Which is still cheap 

I just had my wideglide serviced and apparently the front wheel bearings are a bit noisey (rumbling) they are abs bearings and only done 6000miles, are there better aftermarket ones? how long should the job take to fit bearings? $54 an hour is cheap my local dealer is at least $150 per hour

Some people change out the bearings every second tyre change. My plan is change every 2nd front tyre and every 3rd rear tyre. I can do it myself so no labour cost and I use SKF bearings not genuine Harley