It's a bit unclear to me what you're trying to do, so I'm explaining a few things, and giving you a few options to investigate further, depending on what your purpose is.
The de facto means of synthesizing music on computers uses MIDI (Musical Instrument Digital Interface). Because musicians rarely think directly in terms of frequencies or wavelengths (they count steps or half-steps along a scale), MIDI represents each pitch with an integer, that represents a number of half-steps. By default, MIDI assumes these pitches are tuned using a standard called "12-Tone Equal Temperament" (12TET), and, unfortunately, it isn't particularly easy to make it use other tunings.
What does this mean? And why is it a problem? (I'm not sure how much of this you know already, so I apologize if I'm repeating what you know)
In theory what you say about tuning being based on frequency ratios is 100% absolutely correct -- this is a system called Just Tuning. The major third is a 5/4 ratio and the perfect fifth is a 3/2 ratio. However instruments with fixed-pitches (keyboards, fretted instruments, etc...) are rarely tuned that way in practice. Instead, they compromise, by rounding each note in a chromatic scale to the nearest 12th of an octave. Since an adding octave is equivalent to multiplying the initial frequency by 2, adding a 12th of an octave is the equivalent of multiplying the initial frequency by 2^(1/12). This is how all the half steps on a piano are usually tuned.
So instead of the pure ratios, you would actually have:
- sin(A pi t)
- sin(2^(4/12) A pi t)
- sin(2^(7/12) A pi t)
- sin(2^(12/12) A pi t)
Note: Compare 2^(4/12) ~ 1.26, with 5/4 = 1.25. Also compare 2^(7/12) ~ 1.498, with 3/2 = 1.5.
These are exactly the frequencies that any MIDI synthesizer will play, given the MIDI notes numbered n, n+4, n+7, and n+12. So, if you are only looking to play a chord, and don't care about the frequency ratios being pure (just), you can just use MIDI.
However, if you are looking for something that will play the actual just ratios, it will be a bit trickier. You might start with looking at some of the things here: https://music.stackexchange.com/questions/351/software-that-allows-playing-in-different-temperaments
If you just want to see what they sound like, you can check out this youtube video:
https://www.youtube.com/watch?v=6NlI4No3s0M
If you can write software, you might try writing your own, but I don't want to go into how to do that if that's not going to be helpful.
I'm not sure what kinds of programs you're describing that "only takes Hz as input". Is this a software library (like an API call?) or something different? There are (obviously) API calls that can send more complex data to the soundcard than a single-frequency wave.
EDIT: I've not used it, but it looks like perhaps this software is capable of doing what you want: https://www.youtube.com/watch?v=z0NZQMiDdNU