The time of day will greatly effect the look of the images. The project's location, orientation and weather conditions must also be taken into account. Every project has it's own set of considerations and what looks "good" can be very subjective. Please take the lighting condition into consideration when determining what time is right for your project.
Sunrise is often optimal for Boston since the sun rises over the water. The light quality is best seen from 15 minutes before to 30 minutes after sunrise. It typically has a slightly less colorful quality than sunset and the winds tend to be lighter than in evenings. Often there is a low fog that blows off as the sun rises.
Midday light is often requested when the client prefers the subject and surroundings to be well lit. It is not suggested for cinematic shots but is often preferred for real estate.
The "golden hour" is highly sought after by photographers and filmmakers for it's colorful and dramatic quality. Looking into the sun will give you sun flares while looking away from it may show some harshly lit sections with deep shadows. This look is best suited for those wow shots but may not be the best if you want everything evenly lit.
If you want the city lights along with a dark blue or purple sky, the best time is immediately after sunset during the "blue hour". The drawbacks of twilight shots is that the ISO must be raised in the camera, minimally degrading the image sharpness. Night shots are when all the lights are clearly seen in the buildings.
Cloudy, hazy and overcast days are best for even lighting. It may not be the most exciting scene but everything will be lit properly and the colors of the buildings will pop against the gray/white backdrop of the sky. The shoot can take place during any time of day and look consistent.