Stay calm, soldier. Our scientists have a few suggestions for you.
Liquid ammonia boils at a temperature of −28F (−33C), so any creature with this as its blood will be significantly colder on thermal imaging than a human being. (The alternative for maintaining liquid form, extreme pressure, would make them explode like a balloon from the tiniest of pinpricks, assuming any organic life could have developed to contain such pressures in the first place, so we find it extraordinarily unlikely that they've gone this route in their evolution.) The energy requirements to mask this — by keeping internal temperatures this cold but skin surface temperatures at the human-normal 98F (37C) — would be insane, and would likely drive their metabolism to such extremes that they could not stop eating — a distinctive behavior you could use to your advantage if they do try and mask their thermal signature to mimic yours.
Doing some rough back-of-the-envelope calculations, maintaining a skin temperature of 30C with an internal temperature of −30C (allowing for some pressure and/or additives to let their ammonia-blood stay liquid at slightly warmer temperature) is a difference of 60C. Maintaining this difference therefore requires approximately 250 Joules of energy per gram of mass, which is roughly 1,000 Calories. Now, accounting for insulation efficiency and ambient temperature (most likely around 20C), as well as efficiency of their metabolism to turn consumed calories into refrigeration/heating, they could easily require at least 10,000 Calories per hour, or almost a quarter of a million in a day! Per gram of mass! If they're around a human being's average mass of 65Kg, that's over 16 billion calories per day! Compare that to the USDA suggested intake of 2,000 calories per day, and you can see that your shapeshifters are many orders of magnitude higher just to maintain the temperature of their blood!
There's probably some issues with these calculations, especially taking the raw Joules up to a time-based figure. But this should give you a rough idea of the insane energy requirements your antagonists would have.
Edited to add: Since they have to maintain such a low internal temperature, if you can access the ship's environmental controls you can crank up the heat. You might be a little uncomfortable, sweating at 80F/27C, but those extra few degrees might be enough to literally make their blood boil — something that's pretty much universally fatal!
They're also very likely to have small leaks as their ammonia-blood evaporates minuscule amounts through their skin; this might be too little to detect by the woefully under-developed human sense of smell, but a simple gas detector could very likely detect what would amount to a faint aura of ammonia around the impostors.
Another possibility, if you have access to a spectrograph, is to check for high levels of silicon. It doesn't matter how good they are at mimicking the skin color to your eyes, atoms simply emit light at different wavelengths based on what they are, with silicon looking very different from carbon; even if they could somehow emit carbon's spectral fingerprint, it's extraordinarily unlikely that they could mask their silicon. Of course, this depends on how advanced your spectrography equipment is; if your stuff is little better than early 21st-century, they're bulky and slow, so unless you can convince one to give you a skin sample and wait an hour or two for the analysis results (during which time your legit compatriot could of course be replaced, invalidating the test results anyway!) this isn't likely to work, not unless you've got something far better miniaturized and far more sensitive to get faster readings.
Alternatively, if you could kill the lights and then emit specifically (and only) the wavelength of light that silicon reflects, the shapeshifters would practically glow while everything else was nigh invisible. (As a bonus this means you're essentially invisible to them!) You could play with this a little bit to find a combination of wavelengths that cause the shapeshifters to be visibly distinct while still lighting up everything else to a point that you can still work.
It's also highly probable that you could develop a toxin that specifically targets and breaks down the silicon bonds that make silicon-based life possible without affecting your own carbon-based bonds. Unfortunately, the specifics (and potential side effects) of such a route are unknown to us at this time, as our chemists are all on vacation at the moment.