Accelerating problems

I just bought a 2003 Toyota Tacoma and I sometimes have a problem with accelaration and this doesn't happen all the time. Sometimes (at no particular time) when I hit around 40 MPH the RPM's will raise to 4 or5 and my truck has a hard time gaining any speed. It's almost like the engine is struggling to gain speed. The Toyota dealer can't make my truck act up when they have it in the shop. They have changed the fuel filter, but that still hasn't fixed my issue. Wondering if anyone can find out what the problem is. Please help.

Your shop is guessing, a clogged fuel filter would cause engine speed to slow down. You said your engine is speeding up ("when I hit around 40 MPH the RPM's will raise to 4 or5 and my truck has a hard time gaining any speed.")
Do you have a manual transmission? What gear are you in when this happens? Is it more frequent when going up-hill? If yes to questions 1 & 3 and you are in 4th or 5th gear your clutch is probably slipping. A slipping clutch may be corrected by adjustment but it's usually caused by a worn clutch a new clutch is needed.

Is this a manual trans?