We prove Freidlin-Wentzell type large deviation principles for various rescaled models in populations dynamics that have immigration and possibly harvesting: birth-death processes, Galton-Watson trees, epidemic SI models, and prey-predator models. The proofs are carried out using a general analytic approach based on the well-posedness of a class of associated Hamilton-Jacobi equations. The notable feature for these Hamilton-Jacobi equations is that the Hamiltonian can be discontinuous at the boundary. We prove a well-posedness result for a large class of Hamilton-Jacobi equations corresponding to one-dimensional models, and give partial results for the multi-dimensional setting.