l have an 06 Mustang and I am looking to maximize performance with as little money invested as possible.Which option is better and are there any more cheap modifications that can help maximize horsepower?

move mass air intake 3 inch is closer to engine

Both r good but the cold air intake is a lot cheaper & easier to install. My advice go with JLT CA l its the best u can buy & have it custom painted from JLT for under $200 . Another cheap but a must is Under drive pulleys the give u around 12 Hp & make the engine rev quicker.A tuner is also a must on these cars, the adaptive computer will try & make the car run like stock so take take full of advantage l would buy a handheld tuner from superchips or the diablosport predator.

Thats right vinnie forgot to mention exhaust .
Heres a link to 05+Gt exhaust clips of some of the more popular exhaust brands
http://mustangexhaust.com/forums/soundclips.php?catid=2

Golden 5 pretty hit everything on the head.One more thing you can do is install a catback system and an X or H pipe.The less restrictive mufflers and mid-pipe will free up a few more hp,not to mention the sound or tone your car will take on.Google catback exhaust for your year car,you will find about a hundred of them,good luck.