Filter on where the largest date with LINQ

You can sort the query so that the object with the largest date appears in the front, and then get the first record:

var resultado = (from ci in webDB.T_Controle_Importacao
                                 .OrderByDescending(ci => ci.DataTransacao)
                 where ci.CNPJ == cnpj
                 let dd = EntityFunctions.DiffDays(DateTime.Now, ci.DataTransacao)
                 select dd >= 45 ? 3
                      : dd >= 15 ? 2
                      :            1
                )
                .Take(1);

Note that doing this is it is recommended that you have an index in the column that stores the date in the database , so sorting is not slow.

Order to bring the highest date with orderby field descending

var resultado = (from ci in webDB.T_Controle_Importacao
                    where ci.CNPJ == cnpj
                    let dd = EntityFunctions.DiffDays(DateTime.Now, ci.DataTransacao)
                    orderby ci.DataTransacao descending
                    select dd >= 45 ? 3 : dd >= 15 ? 2 : 1).Take(1);