Recall that there are essentially two purposes to the recordings - a reference base-line of the sounds to be modeled and for use as part of the actual sound model itself.
Recording the base-line essentially requires recording of all the required sounds from a selected reference position (typically the center of the reference platform cabin or if possible at a particular earpoint reference such as the pilot's earpoint). Since the idea is to capture as much of the sound environment, levels and frequencies as possible an Omni-directional mic is the most suitable.
These range from cheap (read: junk) to very expensive. The main characteristics to look for are smooth frequency response (no wild peaks or dips) and reasonable sound-pressure range capability, with low inherent noise. You do not need studio quality necessarily but you should look to professional audio shops and broadcast audio companies to find suitable models. An example is the Audio-Technica AT804 or ATM10a.
Recording particular sounds for possible use in the sound model (such as a blower fan, or hydraulic actuator) requires a microphone that is directional in its pickup pattern. This type of microphone is known as a cardioid mic. More directional microphones are known as hyper-cardioid or super-cardioid indicating increased directionality. Probably the best choice would be a cardioid or hyper-cardioid model. Again look for a smooth frequency response, without peaks or dips, and a good sound pressure level tolerance. An example of this would be the Audio-Technica AT813a.
Be sure to watch out for microphones that need phantom power to operate. These models require power down the microphone line to operate and may not be compatible with the recording equipment chosen or they may require batteries which is one more hassle and potential item to go wrong.
Remember to buy the required connector adaptors to allow the microphone to connect to the recorder. MiniDisc recorders usually use mini-jack connectors, while most high quality microphones commonly use XLR connectors. Adaptors are readily available.
Consider using a "shock-mount" stand adaptor or some method of physically isolating the microphone from equipment, consoles, etc. This avoids transmission of sound directly to the microphone via the casing and potentially ruining the recording.
If you intend to provide commentary on one channel (e.g. the Left mic input) for state data correlation while recording the ambient sounds on the other (Right mic input), you need two mics and associated connectors/adaptor cables. The voice mic, however, does not need to be as high quality.
If you intend to connect one of the mic input channels to an existing intercom system (such as the vehicle intercom system), be sure the mic input is compatible with the source equipment. You may need to connect to the line input as opposed to the mic input depending on audio levels. If you are considering this type of set-up be sure that you have input level control on the line input as well as the mic. You may also need additional interface components such as pads or isolation transformers. Above all, test such a set-up thoroughly and under the same conditions you will make the recordings (e.g. high level ambient noise).