I have been to Masada 3 or 4 times the first with a tour party, the remainder with me acting as the guide for friends and colleagues and always during the Summer months.
I would always recommend the walk up (take plenty of water) and allow plenty of time to wander. It is imposing, it is much larger than perhaps you would surmise from below, but equalkly there is not much shade. However, take your time and see the different areas between the many tourist groups. I would recommend trying to get there either very early or go up for the last few hours of the day and wait until the number of people have fallen away. And if the people startgetting on your nerves look out at the views which on a claer day are outstanding.