First talk to your boss about your hours and find out if indeed they are acceptable. There is a difference between flexible hours and coming in too late.
I have worked in lots of places with flex time. In none of them would 11 am or later have been acceptable unless you worked after midnight the day before. I can recall at least one person who got fired for coming in consistently after 10:30 am even though we had some flex in our work hours. There is such a thing as taking too much flex.
Your co-workers may be trying to tell you that you are violating the organizational culture and that your late hours are annoying to them because they have to wait for you to get in and that you are not being a team player by working such odd hours. They may actually be trying to help you in your career by getting you to move closer to the organizational norms.
You may be causing delays to them that you don't know about. You may be making it so all meetings have to be in the afternoon when they would rather have concentrated work time or that you you get to escape attending when they don't. Just because you like those hours and feel productive does not mean that your co-workers feel the same way.
Next you may feel you are more productive then, but do you coworkers really know that you are staying to work all the hours expected? Sometimes emails at 8 pm will help the perception that you don't work as hard because you come in late. You need to learn to manage your teammates' and boss's perceptions of what you do in order to succeed. You could be perceived as a slacker for coming in late. In my experience, morning people especially feel that way because they are not productive in the late afternoon or later. Think what you can do to make sure you are not perceived that way.
Another thing you could do is sit down privately with the worst offenders and ask them straight up why they have a problem with you coming in later if your boss does not. If they have a real problem, it might come out in this conversation and you can suggest a fix. If they say they are just joking, tell that the joke is no longer funny and and to stop.
How you handle people will depend on your assessment of their personality though. Some people are just jokesters and the best thing to do with them is to joke back and let all they things you say just roll off your back. Other people are trying to get you to conform to organizational norms and they won't stop until you do. Some people uses jokes as a way to bond and some use them as a way to put people down and make you look bad. You need to understand what they are trying to do with the joking before you can respond effectively.
It will help to get a training course on dealing with difficult people or read some books on this topic. Bullies need to be handled differently than jokers or people who just want you to work correctly (in their eyes). You need to do some analysis and ask some questions before you decide what to do.