This applies to all "overworld" locations, usually small islands or isolated beaches that can only be accessed by ship. The collectibles below are not listed in a particular order
Animus Fragments
01: Found in the small island near Abaco Island. You'll come across this after getting the Jackdaw and while on the way to the island.
02: 388, 722 (Northeast of Matanzas, east of Dry Turtoga)
03: 268, 699 (small island south of Dry Tortuga fort)
04: 361, 815
05: On shore of a large island to the north in the Dry Tortuga region.
06: 457, 904 In a small beach on the northern island
07: 723, 739 (Eleuthera) Small island within the restricted area.
08: 495, 675 Uncharted Island, north of Salt Key Bank
09: 513,770 Uncharted Island, northwest of Andrea Island
10: 589, 906 Uncharted Island, North of Abaco Island.
11: 585, 592 Uncharted Island, Southeast of Salt Key Bank
12: 581,659 Uncharted Island, South of Andreas Island
13: 613,535 Beach between Gibara and Jiguey
14: 707, 629 Beach west of Salt Lagoon
15: 819,644 Beach northeast of Salt Lagoon and Southeast of Cat Island
16: 854,598 Small island NE of Crooked Island and NW of Mariguana Island
17: 783,310 small island southeast of Cumberland Bay
18: 167, 504 Small island in the border of Castillo de Jagua and Conttoyor regions
19: 269,481 Small beach west of Pinos Isle
20. At the end of a wreck's bow in a small island southwest of Grand Cayman
21: 153,248 Small island west of Santanillas
22: 105,207 Northwest of Ambergris Key
23: 816, 307 Small island southeast of Punta Guarico fort, northwest of Petite Cavern
24: 965, 144 Beach, far east of Ile a Vache
25: 669, 269 Beach east of Anotto Bay
26: 144,402 East of Tulum, northeast of Chinchorro
27: 278, 293 Southwest of Cayman Sound
28: 51,321 Beach north of Corozal
29: 468,44 West beach of Isla Providencia
30: 549, 167 East of The Blue Hole
Chests
01: 316, 759 (East of Dry Tortuga fort)
02: 462, 797 – Southeast of Florida island
03: 501, 846 – Islet between Florida and Apaco
04: 457, 904 In a small beach on the northern island
05: 674,771 Small island between Nassau and Eleuthera
06: 669, 830 On an uncharted beach, east of Abaco Island.
07: 550, 816 Uncharted island west of Abaco Island
08: 651, 723 Uncharted island south of Nassau, east of Andreas Island
9: 488, 591 Uncharted island south of Salt Key Bank
10: 402, 650 Inlet beach between Matanzas and Salt Key Bank
11: 442,699 Southeast of the San Ignacio Wreck
12: 497, 730 Uncharted island west of Andreas Island.
13: 637,947 Small island, north of Abaco Island
14: 688,904 Small island, northeast of Abaco Island
15: 760, 560 Small island, west of Crooked Island
16: 653, 590 Small island, north of Gibara
17: 707,558 Small island, northeast of Gibara
18: 677, 674 Small island, East of Antocha Wreck
19: 809,597 island southeast of Salt Lagoon and North of Crooked Island.
20: 901,487 Small island northeast of Great Inagua
21: 121, 628 West of Cape Bonavista
22: 58, 535 Beach, West of Conttoyor fort.
23: 121,450 Beach in an island south of Conttoyor
24: 699, 155 uncharted beach east of Kingston
25: 294,408 Small island southwest of Pinos Isle
26: 655,73 Small island southeast of Kingston.
27: 771,98 Small island south of Kabah Ruins
28: 441,385 Small island northwest of Devil's Eye Cavern.
29: 442, 333 Small island east of Grand Cayman
30: 394,199 Small island east of Misteriosa
31: 471,217 Beach south of Charlotte fort.
32: 627,331 Beach of an island southeast of Cabo de Cruz fort and north of Anotto Bay.
33: 410, 503 Small island between San Juan and Castillo de Jagua
34: 832, 387 Small island east of Punta Guarico
35: 951, 364 Beach East of Tortuga
36: 792, 240 Beach northeast of Navassa
37: 800, 192 Beach southeast of Navassa or Northeast of Kabah Ruins
38: 893,174 Beach northeast of Ile a Vache
39: 379,400 Small island, southeast of Pinos Isle
40: 302,572 Beach west of Castillo de Jagua
41: 246,347 Small island between Chinchorro and Cayman Sound
42: 93,292 Southwest of Chinchorro Fort, west of La Concepcion
43: 176,191 Small island, southwest of Santanillas
44: 238,169 Beach southwest of Misteriosa
45: 144, 97 Beach southeast of Ambergris Key
46: 527, 113 East of New Bone in the middle of the ocean.
Secrets
01: Message in a battle (18. My Searche)
669, 830 On an uncharted beach, east of Abaco Island.
02: Message in a bottle (17: Taking My Leave)
798, 191 Beach southeast of Navassa or Northeast of Kabah Ruins
03: Message in a bottle (19: On Being a Sage)
144,98 Beach southeast of Ambergris Key