How to make a safe homemade 3D laser rangefinder
I want to make sure it doesn't blind anyone. How can I ensure this is
  safe for home use?


use a Class 2 laser or lower, that's the only way you can be entirely sure.


  Ideally, I'd like to find a 2.5-5mW infrared line laser, but no one
  seems to sell anything like this.


Sadly, these do not have their place on the market. However a word of caution. just because you cannot see the laser doesn't mean that it cannot do damage. By intentionally making it invisible, you're putting an elephant in the room. Not only do you not know where the dot is with IR, you also cannot tell damage is being done until it is way too late. I recommend a higher wattage (100mw), but in a UV pulse laser. UV lasers are typically regarded as some of the safest lasers there are, as most of the waves at this point can pass through some parts of the body. 


  Could I control a stronger 5V laser's duty cycle by connecting it's +5V lead to an Arduino pin and generate a PWM output of 10% to give a 25mW laser an effective 2.5mW output?


No, like LEDs, lasers need a constant current source, not voltage. Not only will turning the laser on and off quickly shorten the diode's lifespan, it will also skew your rangefinder by inducing pseudo rolling shutter effect.


  Also, what minimum power would I need to make an effect laser rangefinder? Even if I did find a 5mW line laser, would that be bright enough to detect a couple meters away?


Typically, rangefinders will use .5mW/meter- .3mW/meter to the maximum range. if you wanted something that measured an effective 800m, you would use a 240-400mW diode.