You can take advantage of the regular pattern of squares.
I'm assuming the reason this is a bottleneck is because you have to wait while your algorithm finds all squares intersecting any of the triangles and computes all the areas of intersection. So we'll compute all the areas, but in batches for each triangle in order to get the most information from the fewest calculations.
First, as explained by others, for each edge of the triangle, you can find the sequence of squares that edge passes through, as well as the points at which it crosses each vertical or horizontal edge of a square.
Do this for all three sides, keeping a list of all the squares you encounter, but keep only one copy of each square. It may be useful to store the squares in multiple lists, so that all squares on a given row are all kept in the same list.
When you've found all squares the triangle's edges pass through, if two of those squares were on the same row, any squares between those two that are not in the list are completely inside the triangle, so 100% of each of those squares is covered.
For the other squares, the calculation of area can depend on how many vertices of the triangle are in the square (0, 1, 2, or 3) and where the edges of the triangle intersect the sides of the square. You can summarize all the cases in a few pencil-and-paper drawings, and come up with calculations for each one. For example, when an edge of triangle crosses two sides of the square, with one corner of the square on the "outside" side of the edge, that corner is one angle of a small triangle "cut off" by that edge of the larger triangle; use the points of intersection on the square's sides to compute the area of the small triangle and deduct it from the area of the square. If two points instead of one are "outside", you have a trapezoid whose two base lengths are found from the points of intersection, and whose height is the width of the square; deduct its area from the square. If three points are outside, deduct the entire area of the square and then add the area of the small triangle.
One vertex of the large triangle inside the square, three corners of the square outside that angle: draw a line from the remaining corner to the triangle's vertex, so you have two small triangles, deduct the entire square and add those triangles' areas. Two corners of the square outside the angle, draw lines to the vertex to get three small triangles, etc.
I'm phrasing this so that you always assume you start with the entire area of the square and reduce the area by some amount depending on how the edge of the triangle intersects the square. That way, in the case where the edges of the triangle intersect the square more than twice--such as one edge cuts across one corner of the square and another edge cuts across a different corner, you can just deduct the area cut off by the first edge, then deduct the area cut off by the second edge.
This will be a considerable number of special cases, though you can take advantage of symmetry; for example, you don't have to write the complete calculation for "cut off a triangle in one corner" four times.
You'll write a lot more code than if you just took someone's convex-polygon library off the shelf, and you will want to test the living daylights out of it to make sure you didn't forget to code any cases, but once you get it working, it shouldn't take much more effort to make it reasonably fast.