Simply because the water couldn't have gotten into your brain through any orface (nose or mouth or ears, etc), I'd say it's highly unlikely. I think what you may be experiencing is just the sensation of getting some sea water into your sinus's, or the aftermath of that. At worst, I'd say you have a sinus infection. I know it's really easy to jump to extraordinary conclusions involving things like this, but just remember that this kind of this is so rare it's almost unheard of, and you would most definately have a fever if something was eating at your brain as your white blood cells rushed to the area to combat it. You'd also most likely be experiencing a severe, severe, very severe headache and some neurological distress like loss of bladder function or not being able to move your arm/neck. When the brain is attacked by something, even bacterial meningitis, you can't touch your head to your chest and you get very sick, sick to the point where you wouldn't be on the forums questioning it at this point, you'd be calling an ambulance .
I hope this is enough evidence for you against the idea of brain eating amoeba. :) I sincerely doubt you're experiencing that.