Neck/Shoulder Pain

A little more information might help.  Have you been professionally fitted on your bike?  What is your swimming experience?  Have you ever worked with a coach or swimming instructor?

Eliminating these variables as possible causes or contributing factors can be a good starting point.

You also mention that you get this injury 1-2 times a year.  Is that just since you've been a triathlete, or does it go back to before you participated in this sport?

What did you do to get yourself to relax the arms/shoulders.  I have a similar issue on my left shoulder (under the scapula) and have been trying to figure out what to do differently.

I do not have a coach for swimming. I am not new to swimming but I am new to swimming longer distances. I started biking last year on a road bike, before it was a mountain bike. I teach tennis so I periodically get a shoulder issue which is usually in the shoulder blade area that I always attribute to the repetitive motion of serving and hitting tennis balls. I just have had this more times than I normally do over a short period of time and assumed that triathlon training had something to do with it.

I've had neck pain and then soreness each time I've had my bike re-fitted (lost weight and got better on the bike, so position got more aggressive with each fit).  Went away each time, but took time.  Actually, I'm at the end of a month after this fit and it's just starting to get better on long rides, so might be a while to fully adjust (takes HOURS and HOURS on the bike to get used to a change in fit - at least for me, and I suspect for most).

Not to say that's what is causing your pain, but it certainly has worked that way for me.  I find that if I consciously relax my neck and look more in front of the bike (rather than waaaaay down the road all the time) - just peeking up into the distance frequently (safety first, but not always looking 3000m away) it helps.  Can stay aero and still see what's up - just a minor adjustment to head position.

Good luck!

Matt