A choice of recommendation letters

[caconym]

Hi, so I'm a senior studying computer engineering, and applying for PhD programs in computer science. I have two recommendation letters already, one from a PI whom I worked with for my entire undergrad career, and another from a well-known professor I worked with this summer.

Most schools and fellowships require exactly three letters, so I'm not sure what my choice should be here:

1. I could take a joint recommendation letter from two staff scientists I worked with for the last two years. However, since this was still under my school's lab, I think my PI could cover it in her recommendation letter
2. I could take a recommendation from just one of them, since I worked with one for longer than the other, and they are both leads on a project I'm currently working on
3. I could take a third recommendation letter from a mentor at my software development internship, which I did some impromptu research with.

What's the best choice here for a third letter of recommendation? For those that allow more than three, which ones should I include as well?