Aquatic plants have a negatively charged surface. Ammonium is positively charged so it takes less energy for plants to uptake NH4 than NO3 which is negatively charged.
Yes, polarity of the ions is one of the important factors, but the biochemical pathways are far more complex than this simple explanation. Cell membrane physiology as it relates to nutrient uptake is quite interesting. This process is highly regulated by the needs of the cell and different species utilize different strategies for assimilating nitrogen.
The enzyme mediated biochemical reactions that take place inside the cell allow most plants more than one option to assimilate nitrogen from the environment. Depending on the species, NH4+ is more easily assimilated (requiring less energy expenditure) than nitrate, nitrite, urea, or atmospheric N2.
The whole process is quite interesting and worthy of a far deeper discussion than usually takes place on a hobbyist level. If I get a minute, I'll dig into my old texts to see if I can find something that will shed some light on the subject.
For starters, this
goes over just a few of the most basic aspects of nitrogen fixation from the form of N2 to NH4. This doesn't really answer the question of the the preferential source of nitrogen for aquatic plants, but it does shed a bit of light on the complexity of the invovled biochemistry.
The subsequent chapters
address some of the nitrate/ammonium pathways.