My ex husband and I have been separated for 5 years(not legally separated). We have shared our son with him having our son on weekends and I have him on weekdays. For the last 2 years I've been with my boyfriend who now lives in another state with a great job and a house waiting for my son and I. my ex was OK with shared custody, our son with me during the year and with him for the summers... split christmas and spring break alternating years. I wasn't asking for child support just that he pay for flights. All was well until he found out my boyfriend was going to be involved. Now he is fighting for full custody so I can't take our son with me in June... which is when my job starts. My question is would it be easier for me to just leave with our son and file for custody once we are settled in the other state... rather than fight and possibly get stuck in this state where I have no job & soon no home?

The problem with your plan is that your new state won't have jurisdiction over the proceeding for a period, usually 6 months. If he files for custody in that time, you can and most likely will be ordered by the court to return your son to the state.

Running across state lines makes it more complicated, not less.