Remember this is just a season - one that is hard and that you are doing the right things by asking the questions, but it will pass to the next season sooner than you know.
I would urge you not to follow advice that tells you to ignore him. A baby has one means at his disposal to let you know his needs - crying. Until they develop (which is what you want to encourage, not discipline), the mom is the primary provider of those needs - which is what is so hard for us because we don't know!
However, if we teach them (put them in their bed and close the door) that we are not there with them through thick and thin, will they call when their friend is drunk and they need a ride home? Will ignoring their cries teach them we will be there for them when they have cheated on an exam and need to confess and make it right.
When is abandonment taught? Sorry to get on a soapbox, but as moms, we are the only source for tiny babies (even with awesome dads, the primary emotional provider is mom).
On the actual topic, it sounds like in some cases he may be experiencing gas pains, which can be very painful. Have you considered removing milk from your diet and adding proibotics a couple times a day? He could be having bowel issues and that could only grow larger if ignored. You could start taking some good enzymes like Zyme Prime (chewables are yummy and easy to eat) that could really help him if he is having digestive problems.
So good for you that you are breastfeeding - I know the dedication, great job mom!
My hope is that you are educated on the gastrointestional damage shown by many studies now to be results of vaccines and that you have considered altanative schedules to those the CDC has recommended without one single study proving they are safe for babies. If you are not, I would encourage you to delay vaccines until you are able to read. www.generationrescue.com is a good place to start.
Give him a squeeze for me, I miss that little baby boy (mine is now 9 and I don't get nearly the squeezes anymore....).
J.