My son is 6 years old and is having a problem reading, he will be in 2nd grade next year and I want to work with him over the summer. Does anyone know of any good reading programs that work. I looked at the hooked on phonics website, has anyone tried it?

Sounds like a cliche but anything that has a phonics platform (remember ‘Hooked on Phonics!’?). Kids that learn to recognize letters and say what they sound like will learn to read and sound out words (by separating them into sounds) and not learn by memorizing words.
You can probably google the phonics alphabet song that has a tune to learn each letter and its sound.