Determining line of sight is mostly a common sense process, particularly for links in the 0-5 mile range. Here's an overview, along with some helpful pointers:
First, line of sight for microwave (in the licensed bands) simply means that one antenna can "see" the other. Unlike cellular antennas, where the higher they're placed the greater the coverage, with microwave any height beyond what is needed for a point to point connection lends no greater advantage. Licensed microwave also transmits the tightest beam from the antenna, typically only 0.9 to 2 degrees. This is a distinct advantage over unlicensed wireless systems, where the antennas cast a much wider beam (e.g., 6-15+ degrees), consequently requiring greater line of sight clearance.
Checking for line of sight starts with a first hand look from your rooftop. Things look surprisingly different from that vantage. If you can clearly see even a part of your remote building - a window or an elevator penthouse for instance, then it's likely that you have sufficient line of sight. You generally want to see a target of about a ten foot radius. The path must be unobstructed, though power lines are not a problem.
If you don't have line of sight, even off a ladder, then you can fill a weather balloon with helium and float it over your roof, measuring the string when the balloon is visible from your remote location. That measurement would determine the minimum height requirement for the antenna installation. Weather balloons cost about fifteen dollars and are widely available on-line.
There are practical limits as to how high you may place an antenna on your roof. We generally keep to under ten feet, fifteen at a stretch. Higher than that and the antenna mount goes from a simple pipe or tripod to a more substantial "stub" tower, which may introduce aesthetic concerns and often requires a structural analysis for windloading.
If you know that you'll need a ground based monopole or tower, then a crane or bucket truck should be called out to determine the precise height requirement. Maps, GPS systems, path modeling software and other methods are no substitute. For instance, none of these will show tree branches or a billboard that may be in the path. Also don't be fooled by tree lines in fall or winter. A wide gap between trees can easily close in springtime.
If you'd rather not have a tower on your property, then scan the horizon for potential repeater sites. A repeater is simply a relay point that's visible from both your buildings. The repeater can be another rooftop, which is the ideal situation, or else a radio or water tower. While from a technical standpoint any relay site will work the same, a rooftop repeater offers the most convenient access for serviceability.
As for cost of the repeater space, consider whether any of your prospects might offer cut rate or even free roof space based on some business relationship or affiliation. If you're a non-profit, educational or healthcare concern, you may convince the site owner to donate space for a tax deduction, gift in kind or some form of public recognition.
If you have a longer path (8+ miles), then topographic maps are a good way to get a feel for overall feasibility. They're available in software and fun to work with, enabling you to simulate various tower or repeater site possibilities.
We hope these pointers help, though we can't cover every possibility here. Kindly let us know if we may be of assistance.