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I know when a string is plucked on a violin you can hear many overtones at harmonic frequencies, but where do these overtones come from?

Does an ideal string vibrating in a vacuum vibrate at the fundamental and harmonic frequencies? Are the harmonic overtones caused by the shape of the resonating body? Are they from the materials used?

"in a vacuum" will not make sound, but yes your thoughts are on the right track.
All vibrating bodies, strings, plates, beams, etc, have a natural set of harmonics (or overtones as described by some). These are usually determined by the boundary conditions on the vibrating object and a related to the fundamental tone by a simple relationship. For the ideal model of a string fixed at two ends the relationship is

f_n = n*f_1 (f_1 is sometimes called f0, the fundamental).

The fundamental is the lowest frequency of vibration supported by the object and is heard as the natural tone (for example on a properly tuned guitar the open string are named for the fundamental tone).

What excites the harmonics is the attack. Plucking a string at different points will produce completely different sets of allowed harmonics (only those supported by the boundary conditions will show up). Tapping a string or bowing a string will produce different harmonic content and this is what is heard as "tone" by listeners and musicians. Twangy versus warm, smooth, etc. are all adjectives that describe harmonic content.

As for materials, the specific materials do come into play for determining the fundamental but once that is known the harmonic sequence is fixed. For plates and beams the overtones are NOT related by a simple relationship for all boundary conditions. Some vibrating systems can have dissonant overtones. The same applies to pipes, a.k.a horns, and percussion instruments.

What you observe is a physical property of all resonators. In the case of vibration every resonator has different modes of vibration. In the case of a drum head or a cymbal these modes are not harmonic, in the case of strings or air columns the modes of vibration wich are noticeable are harmonic.

Think of a string: It is fixed at both ends if you start and draw on paper the possibilities the string has to vibrate you´ll get one top or valley as the first possibility, one valley and one top as the second, "top valley top" or "valley top valley" as the next one and so on. (In reality a string of a bowed instrument is not moving this way, but thats not important for now)

These are the basic possibilities the string can move and if you don´t take special measures always when the first one is possible, the second and third and ... are possible.

If you take this fact into account the question reverses. How would we expect when we excite the first mode of vibration that there is not even a little energy transfered to the second, third and so on? After all all parts of the string are connected which each other, there are strands in the core and wraps and a bow is not a laser in a super cooled atomic trap so these modes are mechanically coupled.

If you manage to only excite the fundamental mode, the fundamental mode will excite the other ones and so on, simply because its possible to happen.

And thats a basic physical principle: When you transfer energy (e.g. with the bow) all accessible states (modes) will receive there share of it. The one with the lowest energy receives the most, the next one less, the next next one less less and so on. Which one receives how much depends on technique, location of the excitation, material, construction, and so on.

This principle holds true for every kind of excitation. Radio waves, Colors and so on.

In the case of stringed instruments you can make the higher modes of vibration more unfavourable by slightly touching the string effectively reducing the amount of energy that those modes receive that have strong movement in that position and killing those overtones or harmonics. Look for harmonic glissando.

xerotolerant is correct that "overtones" is the correct word in this case. Harmonic and overtone can sometimes be used interchangeably, but not in this case.

This is a big topic, but the short answer is the shape of the wave, which is called the "wave form."

We often depict waves as being simple, smooth curves, but they are, in fact, much more complicated. If you digitally record a sound and then zoom in really, really close, you will see that the wave form is very jagged and irregular. This shape is what gives each instrument its unique characteristics, including the levels of the various harmonics.

So, to answer your specific questions:

Does an ideal string vibrating in a vacuum vibrate with harmonics?

Yes and No, the vibrating string will still create a wave, but the wave will over no medium (i.e. air) to travel through.

Are the harmonics caused by the shape of the resonating body? Are they from the materials used?

Yes to both. All of the properties, e.g. the shape, size, material, performance technique, etc., combine to create the unique sound that you hear.