When it comes to sitars you really don't want to be using a guitar tuner. Sitars, and a lot of Indian instruments, use something called Just Intonation, which is a method of tuning quite different from that of a guitar or a piano.
Just Intonation notes are written as fractions or ratios corresponding to the base note. This means that the resulting notes are purer sounding compared to the rounded up/down version that western music creates.
Have you ever noticed the 'beating' or slight clashing/dissonant sound when you play a complex (or even a simple) chord on a piano or a guitar? This is because the intervals between the pitches are not pure or mathematically correct. The dissonance does add a certain flavour in itself but for Indian music this isn't what we are looking for.
I'm not going to go in to this too far because it is a very deep subject and is not really relevant, but just remember that there is a difference. In western terms, think how a harp sounds almost heavenly and compare that to a piano.
So how do you tune an instrument in Just Intonation? It's actually surprisingly easy to do it by ear because Just Intonation is how we instinctively think two notes should relate together. However, maybe you don't know what you are listening for yet.
The best way to start is probably with a tuner. I don't mean a guitar tuner here (unless it is an advanced one and can do Just Intonation). There are loads of freeware/open source tuners available to download. I used Wintemper for a while, which you can download for free from here - http://wintemper.com/. There is also one called Chromatica which, although isn't free, you can use the evaluation version. This is a bit more flexible to use than Wintemper.
Once you have installed Wintemper, select Just Intonation No.1 from the drop down list on the left. Now you can click on the notes and you should hear the tones in Just Intonation.
I have to say something now though - there are many different types of Just Intonation and not one single standard tuning. The one in Wintemper is good but after a while I noticed that on the sitar the Dha didn't sound quite right.
You can tune this difference quite easily by ear as you should be able to hear that it has a slight beating/dissonance compared to the other notes. The difference is only slight but it will make this note sound a bit striking.
However, if you are starting out with tuning in Just Intonation you can probably ignore this at the moment until you get used to the sound of the new intonation. Or you can edit the temperament or find a tuner where you can input ratios. Email if you need to find out the ratios used for Indian tuning.