Alas whatever you do with those 3 buttons, it's going to be confusing for the user because they are all physically identical. 99% of the remotes I've seen in this century have rocker buttons for the volume control and a differently shaped button (usually smaller, because it's not used as often) for mute. That also allows one to figure out what he's pressing in the dark much easier (without needed a lighted remote). Don't copy the keyboard designs because the volume control is often an afterthought on those, so it's cheaply made with whatever common parts are available. There's also a difference in how one holds a remote in hand vs. holding hands on the keyboard, so even the ideal-case considerations are different between these two devices.
As example of good arrangement I suggest the XBox 360 remote below (image courtesy of Wikipedia).
If you google a bit, you can see that Panasonic, LG etc. use a similar layout. Samsung is similar but different enough that's worth discussing. They normally put the mute where the "TV" button is on the XBox remote above, i.e. alongside the volume up. In the place of the Xbox's "mute", Samsung places the channel list button. The two small buttons in between the rockers are very easy to find in the dark, but the lower one is somewhat easier to press. So I think Samsung made a deliberate choice of making the channel list easier to find than the mute. I suspect they may have conducted some user studies before they decided this, because they use that layout on many different models. But since you don't care about making a full TV remote, you have no competition for your mute button, so place it alongside the lower volume button.
Also since there are no [TV] channels for the user to change in your application, you could place the whole set of buttons further to the right. Look at how some Denon remotes (an expensive and a cheap one) both place the volume buttons to the right side (image from electronicexpressinc.com):
That's because on an audio-oriented product changing channels/tracks (on the radio tuner or CD) doesn't happen as often as one zaps the TV channels. You are however taking some risk in doing this. If your users are very used to TV remotes, they may find this volume-column-to-the-right arrangement "unnatural".