Engine Chugging

I have a 1990 Ski Nautique. Last year it would almost stall coming off the start and had the accelerator pump changed. Works great this year off the start but every second or third time out in the boat it will really chug at low speeds (10-25 mph).....but it is hit and miss....sometimes it runs great all the time and seems to run well at higher speeds. Any suggestions?

Thanks for responding. I will post in the engine section. Last year when I went to take off pulling a skier or otherwise and pushed the throttle down the engine would just about stall......took it to a dealer and they changed the accelerator pump and also did carb work with a carb kit. This year the take off is great but every few times out it chugs badly at lower speeds. For example, today I took the kids skiing first thing and worked great for about 20 minutes and then all of a sudden while driving at about 20 mph pulling my son wake boarding it started chugging again.....I can push the throttle down and it takes off to high speeds but to mantainat a lower speed it seems like it will stall. Thanks for your help.