My daughter and I have flown quite a bit since she was very small. She was 4 months the first time she flew. She is 2 now. This is what has worked for us. She has been both a lap baby and had a seat. If she has a seat, I definitely bring her car seat. You will want the option to put her down, especially if the flight is long. I can't remember for sure what I did with the base when she was younger. I would have either brought it onboard with the car seat, or checked it with the stroller. I think probably, I had it onboard. I kept her in her car seat during take off and landing. I have given her a bottle, nursed her, or used a pacifier to help her ears adjust to the pressure changes. We have never had ear problems with take off or landing. I never was able to nurse her while she was in the car seat. I tried, but my boobs just didn't stretch that far. Some people swear by it, so maybe you want to try that. The timing I use to start my daughter with whatever we are using for pressure relief, is just after the wheels leave the ground and on the way back down, when the flight attendants take their seats. Sometimes, I would wait until I first started feeling the pressure in my own ears. This way, I wouldn't run out of a bottle or have her get filled up too soon. Now that she is 'older', I just use a pacifier and she gets to keep it the whole trip...quite a treat for her because she usually only has it when she sleeps. Bring quiet little toys that your son has not seen before or not seen in a while. You may want to wrap them in cute wrapping paper. I actually have a bag of plane toys, which my daughter sees only when we fly. Unwrapping them keeps her occupied a little longer. I have never used benedryl or anything to help my daughter sleep on a plane, though, once, I had it with me, just in case. We have had so few problems flying and I don't think we have ever really annoyed anyone around me, which is always a fear of mine. I try to sit next to other people with kids. I used to hold her up so she could see other passengers during the flight and usually they would talk to her and entertain her for a while. :) Bring your stroller and check it at the gate. You will have to get a tag for it at the gate counter. Sometimes they bring one to you while waiting in the preboarding line, but check at the counter first. When you go through security, put all of your stuff on the belt first, then the folded stroller and upside-down car seat. They may or may not want you to take your son's shoes off. I wait until they ask. Security has always been very helpful and often the people around me as well, when I am traveling alone with my daughter, so don't let that part stress you. If people are really in a hurry behind you, they will get in a different line. Check online with the airline regarding what they allow you to bring onboard. You should be able to bring baby formula, milk, etc. You will have to bag any medicines, etc. Don't forget your son's birth certificate. You will have to show this at check-in and occasionally at security.
This was long, but knowing what to expect will help you have a more pleasant flight experience. Have a great flight!