I'm guessing you're asking about this year (2018), because next year will be very different given that Star Wars Land is slated to open in the summer.
April: Your dates are probably after the peak Spring Break crowds (Spring Break season tends to peak the two weeks before and week after Easter, given that Easter is on April 1 this year). Now, that being said, Pixar Fest debuts on April 13, so I would expect pretty high crowds in the evenings as folks come in to see PtN in DCA and the new Pixar themed fireworks show in DL. My guess is that the morning and early afternoon crowds won't be too bad on the weekdays (caveat: I don't think there are really any times when things are "dead" in DLR anymore, except perhaps during major downpours). However, I would expect crowds on the weekend days (Fri-Sun) and the in evenings. By that point in April, I would also guess the parks are going towards an off-peak season schedule (at least in terms of opening times).
September: The weather can be hit or miss, but I've been there when it's horribly hot and when it's been pretty nice in September. September crowds are a bit more uncertain because of HalloweenTime. They haven't announced the HalloweenTime dates (probably not until mid-summer), but if you go before the start of HalloweenTime, the crowds might not be bad, but Haunted Mansion and Space are likely to be closed and that parks might be in a state of decorative transition. Once HalloweenTime starts, the crowds really pick-up, especially on weekends. September tends to be considered off-peak season, so the hours and entertainment tend to be reduced on weekdays.
I guess if weather and crowds are the two biggest factors, I would probably lean towards the April dates because of the weather. I don't know that there is a big difference between the dates in terms of crowds.