Since 2.3 version of Gson library the JsonArray class have a 'set' method.
Here's an simple example:
JsonArray array = new JsonArray();
array.add(new JsonPrimitive("Red"));
array.add(new JsonPrimitive("Green"));
array.add(new JsonPrimitive("Blue"));
array.remove(2);
array.set(0, new JsonPrimitive("Yelow"));