Hi,
Both are possible. They have a different shade of meaning.
The first is probably the expression that you would usually use. "I am working on the computer" simply suggests that you are doing some work that is based on the computer. Similarly, you might say, "I did this work on the computer."
You might use the second expression in a more general sense to talk about the activity of working with computers. For example, you might say, "This morning, the pupils are practising working with the computer"; or, "These days, people are more used to working with computers".