Cook pasta, according to package directions, in a large pot of salted boiling water. Drain.
Heat a large skillet over medium high heat. Add bacon and cook until brown and crispy. Remove to a paper towel lined plate and set aside.
Reduce heat to medium, and in the bacon drippings, saute your diced onion until golden brown. Remove to the plate with the bacon.
In a saucepan, melt 3 Tbsp butter. Once melted, whisk in 3 Tbsp flour until it resembles a paste. Cook for 1 minute. Whisk in almond milk and continue whisking until smooth.
Add garlic and thyme and bring to a slight boil. Stir in cheeses, a little at a time, until smooth, a few minutes, and season with salt and pepper, to taste.
Add drained pasta, peas, bacon and onions to the sauce and stir until well combined. Stir in sour cream and hot sauce.