In D&D 5e there are many monsters you could re-skin to make new monsters but if you want to make a new monster that not re-skinned is there a good site to go to or is doing it by hand the best way to go around these things?
There are a number of good resources.
There is official guidance for making your own monsters in the DMG (starting on pg. 273-283). This guidance walks you through each step of making a new monster, as well as a helpful table to determine offensive and defensive stats and abilities by CR (Monster Statistics by Challenge Rating, pg. 274).
I also found The Angry GM's 5-part guide on monster building to be quite insightful in building my own monsters. Not only does he break down the DMG rules and point out their weaknesses, but he also expounds on some of the thought processes involved in making a good monster for a good encounter.
While some software exists to help you make a fancy looking, formatted stat block for your monster, I haven't come across any tools that will help with the actual decisionmaking required in making your own monster.