color isn't a class/object but a primitive type, an int.
Why do you do this conversion?

Wow. Lot of sort out.
First, there is a thread about color sorting: Sort 2d array. There is also a thread about counting colors in an image.
"converting it to an array i could sort"
You can sort ArrayList too. I started to write a Hacks entry about sorting arrays and collections, as the topic surfaces often. I should finish it... :-)
"The code is a following,  but is veeeery slow."
Yes, append() is handy, but extremely slow on large arrays: each time you use it, it copies the entire array to a new one just one unit larger...
"Are ArrayList only for objects"
Yes, that's an irritating limitation of Java Collections. They made objects boxing primitive types mostly for this usage (Integer, Float, Boolean, etc.). Java 1.5 introduced autoboxing to reduce the pain. But it is still costly (size and time). That's why arrays are still useful: small (minimal size), fast access. Good when you know the final size.
"I'm trying to count how many different colors are in pixels array."
Actually, you don't need sorting and such. I would use a HashMap with (boxed) color as keys and occurrence number (boxed too) as value: take color, get it from HashMap. If null, not there yet, put (color, 1) in map. If there, put (color, nb + 1).

Generally speaking, an ArrayList is fast if you are storing and looking up items by a numerical index and a HashMap is fast if you are storing and looking up things by an object identifier.

Philho's recommendation sounds correct to me for your case, since the key is a Color object and the value is a count. Since the value must also be an object, the Integer count has to be converted to an int to increment it, of course, as PhiLho indicated.