I'm not an accountant, but I think you will need to look back at last year and see how much the mortgage interest deducted from your rental income and compare that to what it would look like if two properties did not have that interest and how much the third property now has. It sounds pretty complicated and I think you will have to write it all out and compare last years to what next years would look like, or just call your accountant and ask them to evaluate it for you.
If you already have a lot of loans and want room for more loans it would make sense to have two paid off. Does that factor in at all?
How long have you had the properties and are you currently in a growth phase where you want to acquire more properties or are you in a stage where you want to focus on paying them off and having stable income, for example have you already paid 15 years and want them paid off in 15 years because you plan to retire at that stage?
There are really so many personal decisions that will influence that choice on refinancing.